Stuart J E Baird | Academy of Sciences of the Czech Republic (original) (raw)

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Papers by Stuart J E Baird

Research paper thumbnail of House mouse hybrid zone variability: from a phenotypical point of view

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Research paper thumbnail of Murine Cytomegalovirus in the European House Mouse Hybrid Zone

Murine cytomegalovirus (MCMV) is an enveloped dsDNA virus (family Herpesviridae) which is normall... more Murine cytomegalovirus (MCMV) is an enveloped dsDNA virus (family Herpesviridae) which is normally used to model human cytomegalovirus infection. The host species of MCMV is the house mouse in which the virus produces persistent asymptomatic or latent infections. Two taxa of house mice, Mus musculus musculus and Mus musculus domesticus meet and hybridize along a 2500 km long front streching from Scandinavia to the Black Sea. At this front the taxa form a narrow hybrid zone, a tension zone species barrier. A preliminary study across a transect in the Bavarian/Bohemian part of the house mouse hybrid zone (HMHZ) showed that each mouse taxon carried different MCMV strains. Therefore the HMHZ may serve as a suitable natural system for studying recombination between divergent viral strains, a potentially important natural evolutionary process allowing strains to overcome the host species barrier and to infect a new host taxon. House mouse tissues (especially saliva and salivary glands) were collected across the Bavarian/Bohemian region of the HMHZ to investigate the prevalence of MCMV and for subsequent isolation and genomic characterization of the different viral strains. Molecular screening of 155 saliva samples revealed a prevalence of 83%. A subset of positive individuals were then used for MCMV reactivation in vitro directly from salivary glands and part of the enriched samples were sequenced using the HiSeq 2500 next generation sequencing technology for to obtain the viral genome of MCMV from Mus musculus musculus, not yet available in public database. These data will serve as a basis to study MCMV genomic diversity and recombination in the HMHZ.

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Research paper thumbnail of Murine Cytomegalovirus in the European House Mouse Hybrid Zone- From Field Work to Genome Characterization

Murine cytomegalovirus (MCMV) is an enveloped dsDNA virus (family Herpesviridae) which is normall... more Murine cytomegalovirus (MCMV) is an enveloped dsDNA virus (family Herpesviridae) which is normally used to model human cytomegalovirus infection. The host species of MCMV is the house mouse in which the virus produces persistent asymptomatic or latent infections. Two taxa of house mice, Mus musculus musculus and Mus musculus domesticus meet and hybridize along a 2500 km long front streching from Scandinavia to the Black Sea. At this front the taxa form a narrow hybrid zone, a tension zone species barrier. A preliminary study across a transect in the Bavarian/Bohemian part of the house mouse hybrid zone (HMHZ) showed that each mouse taxon carried different MCMV strains. Therefore the HMHZ may serve as a suitable natural system for studying recombination between divergent viral strains, a potentially important natural evolutionary process allowing strains to overcome the host species barrier and to infect a new host taxon. House mouse tissues (especially saliva and salivary glands) were collected across the Bavarian/Bohemian region of the HMHZ to investigate the prevalence of MCMV and for subsequent isolation and genomic characterization of the different viral strains. Molecular screening of 155 saliva samples revealed a prevalence of 83%. A subset of positive individuals were then used for MCMV reactivation in vitro directly from salivary glands and part of the enriched samples were sequenced using the HiSeq 2500 next generation sequencing technology for to obtain the viral genome of MCMV from Mus musculus musculus, not yet available in public database. These data will serve as a basis to study MCMV genomic diversity and recombination in the HMHZ.

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Research paper thumbnail of Review for "Genetic traces of hybrid zone movement across a fragmented habitat

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Research paper thumbnail of Historical demography and climatic niches of the Natal multimammate mouse (Mastomys natalensis) in the Zambezian region

Mammalian Biology

The Natal multimammate mouse (Mastomys natalensis) is the most widespread rodent species in sub-S... more The Natal multimammate mouse (Mastomys natalensis) is the most widespread rodent species in sub-Saharan Africa, often studied as an agricultural pest and reservoir of viruses. Its mitochondrial (Mt) phylogeny revealed six major lineages parapatrically distributed across open habitats of sub-Saharan Africa. In this study we used 1949 sequences of the mitochondrial cytochrome b gene to elaborate on distribution and evolutionary history of three Mt lineages inhabiting the open habitats of the Zambezian region (corresponding roughly to the African savannas south of the Equator). We describe in more detail contact zones between the lineages—their location and extent of co-occurrence within localities—and infer past population trends. The estimates are interpreted in the light of climatic niche models. The lineages underwent reduction in effective population size during the last glacial, but they spread widely after that: two of them after the last glacial maximum and the last one in mid-...

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Research paper thumbnail of Genomic evidence of paternal genome elimination in the globular springtail <i>Allacma fusca</i>

bioRxiv (Cold Spring Harbor Laboratory), Nov 14, 2021

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Research paper thumbnail of Subspecific rodent taxa as the relevant host taxonomic level for mammarenavirus host specificity

Virology, Apr 1, 2023

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Research paper thumbnail of Biogeographical Importance of the Livingstone Mountains in Southern Tanzania: Comparative Genetic Structure of Small Non-volant Mammals

Frontiers in Ecology and Evolution, Jan 18, 2022

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Research paper thumbnail of Rozmanizost hybridní zóny myši domácí: porovnání různých transektů

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Research paper thumbnail of Rise of oceanographic barriers in continuous populations of a cetacean: the genetic structure of harbour porpoises in Old World waters

BMC Biology, Jul 25, 2007

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Research paper thumbnail of Shifting Paradigms for Studying Parasitism in Hybridising Hosts: Response to Theodosopoulos, Hund, and Taylor

Trends in Ecology and Evolution, May 1, 2019

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Research paper thumbnail of Genomic evidence of paternal genome elimination in the globular springtail <i>Allacma fusca</i>

Genetics, Aug 10, 2022

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Research paper thumbnail of The impact of high-throughput sequencing technology on speciation research: maintaining perspective

Journal of Evolutionary Biology, Aug 1, 2017

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Research paper thumbnail of Supplementary material from "The impact of global selection on local adaptation and reproductive isolation

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Research paper thumbnail of A Comparison of Multilocus Clines Maintained by Environmental Adaptation or by Selection Against Hybrids

Genetics, 1999

There has recently been considerable debate over the relative importance of selection against hyb... more There has recently been considerable debate over the relative importance of selection against hybrids (“endogenous” selection) vs. adaptation to different environments (“exogenous”) in maintaining stable hybrid zones and hence in speciation. Single-locus models of endogenous and exogenous viability selection generate clines of similar shape, but the comparison has not been extended to multilocus systems, which are both quantitatively and qualitatively very different from the single-locus case. Here we develop an analytical multilocus model of differential adaptation across an environmental transition and compare it to previous heterozygote disadvantage models. We show that the shape of clines generated by exogenous selection is indistinguishable from that generated by endogenous selection. A stochastic simulation model is used to test the robustness of the analytical description to the effects of drift and strong selection, and confirms the prediction that pairwise linkage disequili...

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Research paper thumbnail of Applications of Junction Theory

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Research paper thumbnail of A dense linkage map for a large repetitive genome: discovery of the sex-determining region in hybridising fire-bellied toads (Bombina bombinaandB. variegata)

Hybrid zones that result from secondary contact between diverged populations offer unparalleled i... more Hybrid zones that result from secondary contact between diverged populations offer unparalleled insight into the genetic architecture of emerging reproductive barriers and so shed light on the process of speciation. Natural selection and recombination jointly determine their dynamics, leading to a range of outcomes from finely fragmented mixtures of the parental genomes that facilitate introgression to a situation where strong selection against recombinants retains large unrecombined genomic blocks that act as strong barriers to gene flow. In the hybrid zone between the fire-bellied toadsBombina bombinaandB. variegata(Anura: Bombinatoridae), two anciently diverged and ecologically distinct taxa meet and produce abundant, fertile hybrids. The dense linkage map presented here enables genomic analysis of the selection-recombination balance that keeps the two gene pools from merging into one. We mapped 4,775 newly developed marker loci from bait-enriched genomic libraries in F2 crosses....

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Research paper thumbnail of A gene copy number arms race in action: X,Y-chromosome transmission distortion across a species barrier

Evolution

A remarkable gene copy number (CN) arms race system has recently been described in laboratory mic... more A remarkable gene copy number (CN) arms race system has recently been described in laboratory mice, where Slx;Slxl1 and Sly genes compete over transmission by altering the fertilization success of X and Y chromosome-bearing sperm, respectively. Here, we focus on this system in nature, where natural selection can counter CN/gene product escalation. Our model is house mouse subspecies hybridizing in Europe. In some regions, Y chromosomes of the Eastern subspecies have introgressed onto Western genomic backgrounds, accompanied by sex ratio distortion in favor of males, consistent with the inbred lines suggested mechanism: Overabundance of SLY protein expressed by invading Y chromosomes. We take Slx as representative of the X side of this arms race and measure Slx|Sly CN and expression across an “Invasion” transect where Ys introgress and a “Control” transect with negligible introgression. Since we found similar Slx|Sly ratios in both transects, SLY overabundance is unlikely to explain ...

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Research paper thumbnail of Copy number variation of the putative speciation genes in the European house mouse hybrid zone

Hybrid zones have long been described as “windows on the evolutionary process”, and studying them... more Hybrid zones have long been described as “windows on the evolutionary process”, and studying them has become even more important since the advance in the genome analysis tools. The hybrid zone between two subspecies of the house mouse (Mus musculus musculusandMus m. domesticus) is a unique model speciation system to study fine scale interactions of recently diverged genomes. Here, we explore the role of gene Copy Number Variation in shaping the barrier to introgression in the hybrid zone within a previously established transect in Central Europe. The CNV of seven pre-selected candidate genes was determined via droplet-digital PCR and analyzed in the context of ~500k SNPs, with the ancestral population (i.e.musculusordomesticus) of every SNP allele previously inferred in the admixed individuals (Baird et al.,in prep.). The copy numbers of five genes were clearly associated with the prevalence of eithermusculusordomesticusgenomes across the hybrid zone. In three cases, the highest and...

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Research paper thumbnail of Table_S1_online

Frequencies of M. m. musculus alleles for each locus and sampling site. Distance along the transe... more Frequencies of M. m. musculus alleles for each locus and sampling site. Distance along the transect and effective number of alleles (Ne) are also given. h = hybrid index expressed as the frequency of musculus alleles averaged across the six diagnostic allozyme loci

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Research paper thumbnail of House mouse hybrid zone variability: from a phenotypical point of view

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Research paper thumbnail of Murine Cytomegalovirus in the European House Mouse Hybrid Zone

Murine cytomegalovirus (MCMV) is an enveloped dsDNA virus (family Herpesviridae) which is normall... more Murine cytomegalovirus (MCMV) is an enveloped dsDNA virus (family Herpesviridae) which is normally used to model human cytomegalovirus infection. The host species of MCMV is the house mouse in which the virus produces persistent asymptomatic or latent infections. Two taxa of house mice, Mus musculus musculus and Mus musculus domesticus meet and hybridize along a 2500 km long front streching from Scandinavia to the Black Sea. At this front the taxa form a narrow hybrid zone, a tension zone species barrier. A preliminary study across a transect in the Bavarian/Bohemian part of the house mouse hybrid zone (HMHZ) showed that each mouse taxon carried different MCMV strains. Therefore the HMHZ may serve as a suitable natural system for studying recombination between divergent viral strains, a potentially important natural evolutionary process allowing strains to overcome the host species barrier and to infect a new host taxon. House mouse tissues (especially saliva and salivary glands) were collected across the Bavarian/Bohemian region of the HMHZ to investigate the prevalence of MCMV and for subsequent isolation and genomic characterization of the different viral strains. Molecular screening of 155 saliva samples revealed a prevalence of 83%. A subset of positive individuals were then used for MCMV reactivation in vitro directly from salivary glands and part of the enriched samples were sequenced using the HiSeq 2500 next generation sequencing technology for to obtain the viral genome of MCMV from Mus musculus musculus, not yet available in public database. These data will serve as a basis to study MCMV genomic diversity and recombination in the HMHZ.

Bookmarks Related papers MentionsView impact

Research paper thumbnail of Murine Cytomegalovirus in the European House Mouse Hybrid Zone- From Field Work to Genome Characterization

Murine cytomegalovirus (MCMV) is an enveloped dsDNA virus (family Herpesviridae) which is normall... more Murine cytomegalovirus (MCMV) is an enveloped dsDNA virus (family Herpesviridae) which is normally used to model human cytomegalovirus infection. The host species of MCMV is the house mouse in which the virus produces persistent asymptomatic or latent infections. Two taxa of house mice, Mus musculus musculus and Mus musculus domesticus meet and hybridize along a 2500 km long front streching from Scandinavia to the Black Sea. At this front the taxa form a narrow hybrid zone, a tension zone species barrier. A preliminary study across a transect in the Bavarian/Bohemian part of the house mouse hybrid zone (HMHZ) showed that each mouse taxon carried different MCMV strains. Therefore the HMHZ may serve as a suitable natural system for studying recombination between divergent viral strains, a potentially important natural evolutionary process allowing strains to overcome the host species barrier and to infect a new host taxon. House mouse tissues (especially saliva and salivary glands) were collected across the Bavarian/Bohemian region of the HMHZ to investigate the prevalence of MCMV and for subsequent isolation and genomic characterization of the different viral strains. Molecular screening of 155 saliva samples revealed a prevalence of 83%. A subset of positive individuals were then used for MCMV reactivation in vitro directly from salivary glands and part of the enriched samples were sequenced using the HiSeq 2500 next generation sequencing technology for to obtain the viral genome of MCMV from Mus musculus musculus, not yet available in public database. These data will serve as a basis to study MCMV genomic diversity and recombination in the HMHZ.

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Research paper thumbnail of Review for "Genetic traces of hybrid zone movement across a fragmented habitat

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Research paper thumbnail of Historical demography and climatic niches of the Natal multimammate mouse (Mastomys natalensis) in the Zambezian region

Mammalian Biology

The Natal multimammate mouse (Mastomys natalensis) is the most widespread rodent species in sub-S... more The Natal multimammate mouse (Mastomys natalensis) is the most widespread rodent species in sub-Saharan Africa, often studied as an agricultural pest and reservoir of viruses. Its mitochondrial (Mt) phylogeny revealed six major lineages parapatrically distributed across open habitats of sub-Saharan Africa. In this study we used 1949 sequences of the mitochondrial cytochrome b gene to elaborate on distribution and evolutionary history of three Mt lineages inhabiting the open habitats of the Zambezian region (corresponding roughly to the African savannas south of the Equator). We describe in more detail contact zones between the lineages—their location and extent of co-occurrence within localities—and infer past population trends. The estimates are interpreted in the light of climatic niche models. The lineages underwent reduction in effective population size during the last glacial, but they spread widely after that: two of them after the last glacial maximum and the last one in mid-...

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Research paper thumbnail of Genomic evidence of paternal genome elimination in the globular springtail <i>Allacma fusca</i>

bioRxiv (Cold Spring Harbor Laboratory), Nov 14, 2021

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Research paper thumbnail of Subspecific rodent taxa as the relevant host taxonomic level for mammarenavirus host specificity

Virology, Apr 1, 2023

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Research paper thumbnail of Biogeographical Importance of the Livingstone Mountains in Southern Tanzania: Comparative Genetic Structure of Small Non-volant Mammals

Frontiers in Ecology and Evolution, Jan 18, 2022

Bookmarks Related papers MentionsView impact

Research paper thumbnail of Rozmanizost hybridní zóny myši domácí: porovnání různých transektů

Bookmarks Related papers MentionsView impact

Research paper thumbnail of Rise of oceanographic barriers in continuous populations of a cetacean: the genetic structure of harbour porpoises in Old World waters

BMC Biology, Jul 25, 2007

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Research paper thumbnail of Shifting Paradigms for Studying Parasitism in Hybridising Hosts: Response to Theodosopoulos, Hund, and Taylor

Trends in Ecology and Evolution, May 1, 2019

Bookmarks Related papers MentionsView impact

Research paper thumbnail of Genomic evidence of paternal genome elimination in the globular springtail <i>Allacma fusca</i>

Genetics, Aug 10, 2022

Bookmarks Related papers MentionsView impact

Research paper thumbnail of The impact of high-throughput sequencing technology on speciation research: maintaining perspective

Journal of Evolutionary Biology, Aug 1, 2017

Bookmarks Related papers MentionsView impact

Research paper thumbnail of Supplementary material from "The impact of global selection on local adaptation and reproductive isolation

Bookmarks Related papers MentionsView impact

Research paper thumbnail of A Comparison of Multilocus Clines Maintained by Environmental Adaptation or by Selection Against Hybrids

Genetics, 1999

There has recently been considerable debate over the relative importance of selection against hyb... more There has recently been considerable debate over the relative importance of selection against hybrids (“endogenous” selection) vs. adaptation to different environments (“exogenous”) in maintaining stable hybrid zones and hence in speciation. Single-locus models of endogenous and exogenous viability selection generate clines of similar shape, but the comparison has not been extended to multilocus systems, which are both quantitatively and qualitatively very different from the single-locus case. Here we develop an analytical multilocus model of differential adaptation across an environmental transition and compare it to previous heterozygote disadvantage models. We show that the shape of clines generated by exogenous selection is indistinguishable from that generated by endogenous selection. A stochastic simulation model is used to test the robustness of the analytical description to the effects of drift and strong selection, and confirms the prediction that pairwise linkage disequili...

Bookmarks Related papers MentionsView impact

Research paper thumbnail of Applications of Junction Theory

Bookmarks Related papers MentionsView impact

Research paper thumbnail of A dense linkage map for a large repetitive genome: discovery of the sex-determining region in hybridising fire-bellied toads (Bombina bombinaandB. variegata)

Hybrid zones that result from secondary contact between diverged populations offer unparalleled i... more Hybrid zones that result from secondary contact between diverged populations offer unparalleled insight into the genetic architecture of emerging reproductive barriers and so shed light on the process of speciation. Natural selection and recombination jointly determine their dynamics, leading to a range of outcomes from finely fragmented mixtures of the parental genomes that facilitate introgression to a situation where strong selection against recombinants retains large unrecombined genomic blocks that act as strong barriers to gene flow. In the hybrid zone between the fire-bellied toadsBombina bombinaandB. variegata(Anura: Bombinatoridae), two anciently diverged and ecologically distinct taxa meet and produce abundant, fertile hybrids. The dense linkage map presented here enables genomic analysis of the selection-recombination balance that keeps the two gene pools from merging into one. We mapped 4,775 newly developed marker loci from bait-enriched genomic libraries in F2 crosses....

Bookmarks Related papers MentionsView impact

Research paper thumbnail of A gene copy number arms race in action: X,Y-chromosome transmission distortion across a species barrier

Evolution

A remarkable gene copy number (CN) arms race system has recently been described in laboratory mic... more A remarkable gene copy number (CN) arms race system has recently been described in laboratory mice, where Slx;Slxl1 and Sly genes compete over transmission by altering the fertilization success of X and Y chromosome-bearing sperm, respectively. Here, we focus on this system in nature, where natural selection can counter CN/gene product escalation. Our model is house mouse subspecies hybridizing in Europe. In some regions, Y chromosomes of the Eastern subspecies have introgressed onto Western genomic backgrounds, accompanied by sex ratio distortion in favor of males, consistent with the inbred lines suggested mechanism: Overabundance of SLY protein expressed by invading Y chromosomes. We take Slx as representative of the X side of this arms race and measure Slx|Sly CN and expression across an “Invasion” transect where Ys introgress and a “Control” transect with negligible introgression. Since we found similar Slx|Sly ratios in both transects, SLY overabundance is unlikely to explain ...

Bookmarks Related papers MentionsView impact

Research paper thumbnail of Copy number variation of the putative speciation genes in the European house mouse hybrid zone

Hybrid zones have long been described as “windows on the evolutionary process”, and studying them... more Hybrid zones have long been described as “windows on the evolutionary process”, and studying them has become even more important since the advance in the genome analysis tools. The hybrid zone between two subspecies of the house mouse (Mus musculus musculusandMus m. domesticus) is a unique model speciation system to study fine scale interactions of recently diverged genomes. Here, we explore the role of gene Copy Number Variation in shaping the barrier to introgression in the hybrid zone within a previously established transect in Central Europe. The CNV of seven pre-selected candidate genes was determined via droplet-digital PCR and analyzed in the context of ~500k SNPs, with the ancestral population (i.e.musculusordomesticus) of every SNP allele previously inferred in the admixed individuals (Baird et al.,in prep.). The copy numbers of five genes were clearly associated with the prevalence of eithermusculusordomesticusgenomes across the hybrid zone. In three cases, the highest and...

Bookmarks Related papers MentionsView impact

Research paper thumbnail of Table_S1_online

Frequencies of M. m. musculus alleles for each locus and sampling site. Distance along the transe... more Frequencies of M. m. musculus alleles for each locus and sampling site. Distance along the transect and effective number of alleles (Ne) are also given. h = hybrid index expressed as the frequency of musculus alleles averaged across the six diagnostic allozyme loci

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